SNAP output for PDB entry 4fth [SNAP web server]

PDB-id

4fth; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription regulator-DNA

Method

X-ray (3.004 Å)

Summary

Crystal structure of ntrc4 DNA-binding domain bound to double-stranded DNA

Reference

Vidangos NK, Heideker J, Lyubimov A, Lamers M, Huo Y, Pelton JG, Ton J, Gralla J, Berger J, Wemmer DE (2014): "DNA Recognition by a sigma (54) Transcriptional Activator from Aquifex aeolicus." J.Mol.Biol., 426, 3553-3568. doi: 10.1016/j.jmb.2014.08.009.

Abstract

Transcription initiation by bacterial σ(54)-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally characterized DBDs from activators all belong to the Fis (factor for inversion stimulation) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DBD of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85bp) from the start of the lpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for σ(54) regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145-binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homolog, Fis. The greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.